‘Junk’ DNA: evolutionary discards or God’s tools?

Summary

‘Junk’ DNA is thought by evolutionists to be useless DNA leftover from
past evolutionary permutations. According to the selfish or parasitic DNA theory,
this DNA persists only because of its ability to replicate itself, or perhaps because
it has randomly mutated into a form advantageous to the cell. The types of junk
DNA include introns, pseudogenes, and mobile and repetitive DNAs. But now many of
the DNA sequences formerly relegated to the junk pile have begun to obtain new respect
for their role in genome structure and function, gene regulation and rapid speciation.
On the other hand, there are examples of what seem to be true junk DNAs, sequences
that had lost their functions, either to mutational inactivation that could have
occurred post-Fall, or by God-ordained time limits set on their functions.

Criteria are presented by which to identify legitimate junk DNA, and to try to decipher
the genetic clues of how genomes function now and in the past, when rates of change
of genomes may have been very different. The rapid, catastrophic changes in the
earth caused by the Flood may also have been mirrored in genomes, as each species
had to adapt to post-Flood conditions. A new creationist theory may explain how
this rapid diversification came about by the changes caused by repetitive and mobile
DNA sequences. The so-called ‘junk’ DNAs that have perplexed creationists
and evolutionary scientists alike may be the very elements that can explain the
mechanisms by which God is at work in His creation now and in the past.

* Terms marked with an asterisk are defined in the Glossary at the end of this article.

The last decade of the 20th century has seen an explosion in research into the structure
and function of the DNA in genomes of a wide range of organisms. As of April 2000,
the whole genomes, or full DNA complements of over 600 organisms have been sequenced
or mapped.1

The sequence of the fruit fly genome, just completed, has over 130 million base
pairs (bp) and is the largest genome sequenced so far.2 The first complete
human chromosome has been sequenced,3 and the Human Genome Project expects
to complete its work sometime in 2003, as does the Mouse Genome Project. Researchers
in the new field of genomics—the comparison of the structures, functions and
hypothetical evolutionary relationships of the world’s life-forms—are
working furiously to deal with the huge inflow of data. Now more than ever, scientists
can see at the most basic level the similarities and differences of organisms, and
are seeking to understand how the blueprints of cells are decoded and regulated.

A major goal of genomic studies is to understand the role, if any, of the various
classes of so-called ‘junk’ DNA. Junk or ‘selfish’ DNA is
believed to be largely parasitic in nature, persisting in the genomes of higher
organisms as ‘evolutionary remnants’ by their ability to reproduce and
spread themselves, or perhaps because they have supposedly mutated into a function
the cell can use.

Origin of the junk DNA hypothesis

The idea that a large portion of the genomes of eukaryotes*4 is made up of useless evolutionary remnants
comes from the problem known as the ‘c-value paradox’, ‘c’
meaning the haploid* chromosomal
DNA content. There is an extraordinary degree of variation in genome size between
different eukaryotes, which does not correlate with organismal complexity or the
numbers of genes that code for proteins. For instance, the newt Triturus cristatus
has around six times as much DNA as humans, who have about 7.5 times as much as
the pufferfish Fugu rubripes.5 The c-value between different
frog species can differ by as much as 100-fold.6 Early DNA-RNA hybridisation* studies and recent
genome sequencing results have confirmed that >90% of the DNA of vertebrates
does not code for a product. Much of this variation is due to non-coding (i.e. not
producing an RNA or protein product), often very simple, repeated sequences. With
the discovery that many of these sequences seemed to have arisen from mobile DNAs
which are able to reproduce themselves, the selfish or parasitic DNA hypothesis
was born.7,8 This said that these sequences served no function in the
host organism, but were simply carried on the genome by their ability to replicate
or spread copies of themselves within and even between genomes.

Plasterk stated it this way when he wrote about transposons*, one of the ‘junk’ DNA types:

‘This ability to replicate is a sufficient raison d’etre for
transposons; they have the same reason for living as, say, the readership of Cell:
none. They exist not because they are good, pretty, or intelligent, but because
they survive.’ 9

Just as Plasterk was wrong about our reason for living, he is wrong about the purposes
of these DNA sequences. Recent research has begun to show that many of these useless-looking
sequences do have a function, and that they may have played a role in intrabaraminic10
(‘within-kind’) diversification.

Types of junk DNA

There are four major kinds of junk DNA:

introns, internal segments in genes that are removed at the RNA level;

Introns

Figure 1. Only portions of a eukaryotic gene code for a protein product.

After most eukaryotic genes and a very few prokaryotic* (bacterial) genes are transcribed, or copied into RNA,
there are segments that are cut out of the messenger RNA (mRNA) before it is used
as a template to make a protein (Figure 1). Introns in fact form the majority of
the sequence of most genes, as was seen when human chromosome 22 was sequenced (Table
1). Why are these RNA pieces present if they are only to be discarded? Evolutionary
theory tries to explain these as vestigial sequences, or that they are useful only
as sites at which recombination can safely take place to reshuffle exons (coding
or protein making segments) into new proteins or new forms of these proteins. Their
ubiquity in eukaryotes argues that they are not post-Fall aberrations, but designed
features.

What then, could these throwaway segments be doing? There are several possibilities
emerging from recent research. One general regulatory role may be to slow down the
rate of translation*, as
the splicing* process does take
time. Alternative splicing allows greater diversity, as certain exons can be skipped
and spliced out to allow a different protein to be made from the same mRNA, as is
seen in some viruses and in the generation of diversity in antibodies. Another example
is the CD6 gene, which is involved in T cell stimulation. Variable splicing of exons
gives rise to at least five different forms of the protein, which allows regulation
of its activity.11

Another observed mechanism by which introns can regulate gene activity is through
the binding of the snipped-out intron RNA to DNA or RNA. There are now a few examples
of the role of introns in regulating the genes they are in, as well as other genes.
One interesting example is the lin-4 gene intron from the nematode Caenorhabditis
elegans. A developmental control gene was found to reside in the intron
of another gene (Figure 2).12,13 The small RNA encoded by lin-4
binds to the mRNA of another developmental gene, lin-14, blocking its ability
to make protein. The binding site in lin-14 was in another supposedly useless
stretch of RNA, the 3' untranslated region (3’UTR*)
found after the last coding region. It was later found that lin-4 RNA also
binds to the 3’UTR in another gene in the developmental pathway, lin-28.14
In fact, more and more cases of 3’UTRs performing gene regulatory activities
have been observed.15,16

There are examples of protein-encoding genes within introns of other genes that
have been recently discovered. For example, on human chromosome 22, the 61-kilobase
(kb) TIMP3 gene, which is involved in macular degeneration, lies within a 268-kb
intron of the large SYN3 gene, and the 8.5-kb HCF2 gene lies within a 27.5-kb intron
of the PIK4CA gene.3

1. All other types of interspersed repeats seen, not detailed here.
2. Tandem repeats from 2 to 5 bp in length (microsatellite DNA). It is estimated
that most of the remaining DNA not sequenced is satellite DNA, as tandem repeats
are mostly located in the heterochromatin, which was not sequenced.
3. Includes all tandem and interspersed repeat types.

Some introns also play a role in mRNA editing, a process where the A (adenine) residues
in the mRNA are changed to G (guanine).17 Self-complementary* or exon-complementary intron sequences, can bind
to each other to form a hairpin loop structure, allowing the sequence of the RNA
to be changed after transcription*
from the DNA. Thus introns can cause new messages to arise from a gene without altering
its DNA coding sequences.

The most general function of introns may be to stabilize closed chromatin* structures in, and around, genes and their associated
regulatory DNA elements.18,19 An isochore*
is an approximately 300-kb segment of DNA whose base pair composition is uniform
above a 3-kb level, for example 67% A-T bp.20 The general ability of
an isochore to be transcribed is dependent on the accessibility of its DNA, i.e.
how tightly histones* and other
DNA-binding proteins wrap up the DNA. This is seen as being at least partially dependent
on the A-T or G-C bp content of a segment of DNA. Though this content can be skewed
somewhat by the choice of triplet codons*
used in the coding DNA (since the code is redundant21), exons are still
constrained in their ability to vary the bp content. The presence of introns throughout
genes allows the proper levels to be maintained, and indeed introns reflect the
general isochore type much more closely than the coding regions. The presence of
introns may well be a condition for at least some forms of sectorial repression
like superrepression, where large sections of chromatin are altered to turn off
groups of cell-type-specific genes or developmental genes. It was shown, for example,
that the gene for rat growth hormone, when deprived of its introns, was no longer
able to form its normal more condensed structure when reinserted back into cells.22

It is important to know whether the specific sequence of an intron is required for
its function when constructing phylogenetic or family trees, or when determining
baraminic* placement of an organism.
In evolutionary studies, DNA sequence comparisons are used to try to build phylogenetic
trees to trace ancestors to descendants. Since introns are generally believed to
be free from the constraints of functionality when mutations cause changes in their
sequence, introns in a particular gene are often compared between organisms, with
the bp differences seen between their sequences supposedly indicating the degree
and time of divergence since they last shared a common ancestor. In some instances,
the assumption that an intron is likely to have mutated freely and extensively during
the presumed millions of years of evolutionary history has proved wrong. Koop and
Hood found that the DNA of the T cell receptor complex, a crucial immune system
protein, is 71% identical between humans and mice over a stretch of 98-kb of DNA.
This was an unexpected finding, as only 6% of the region encodes protein, while
the rest consists of introns and non-coding regions around the gene.23
Does it follow then that we have a recent common ancestor with mice? Since this
does not fit in with evolutionary theory, the authors conclude instead that the
region must have specific functions that place constraints on the fixation of mutations.
This illustrates that DNA sequence comparisons to establish evolutionary relationships
are not the independent tests that they are claimed to be. If the data do not support
the desired evolutionary theory, ad hoc explanations of altered rates of
mutation, functional constraints, etc., can be brought in to explain away discrepancies.24

Another example of selective interpretation of DNA sequence comparison data using
introns is the study of an intron in an important sperm maturation gene on the Y
chromosome of humans.25,26 It was hoped that the ancestry of modern humans
could be traced by sequencing this 729-bp intron from 38 different men from different
ethnic groups. Surprisingly, all 38 men had exactly the same sequence, which was
then interpreted as a ‘recent’ common ancestor (27,000–270,000
years ago) for the whole human race, or possibly that the intron had functional
constraints on its mutability. This latter premise was rejected by the authors because
the sequence of the same intron in chimp, gorilla and orangutan was progressively
more different. These data would strongly support the biblical creationist view
that there was a severe bottleneck in the human population when the Flood reduced
the varieties of Y chromosomes to the one shared by Noah and his sons. Apes would
not be expected to have exactly the same sequence as humans, as they are from separate
created kind(s). The fact that they do have a similar intron argues for a function
for this sequence, and the intron may have been originally created slightly different
for proper function in an ape versus a human.

Thus evidence is mounting to support the important role of introns in gene regulation
and chromosome structure, which would remove 8.15%27 of the junk DNA
of the human genome from the trash heap.

Occasionally located near functional genes or gene families, there are sequences
that very closely resemble other functional genes, but have been inactivated in
someway. Some have a mobile element inserted in their open reading frames (ORFs*), others seem to be ‘processed’
genes, i.e. they look as though the RNA from another gene has been reverse transcribed
(RNA used as a template to make DNA) and reinserted back into the DNA (Figure 3).
A processed pseudogene*
thus precisely lacks the introns, possesses 3'-terminal poly-(A) tracts*, and lacks the upstream promoter* sequence required for transcription of the corresponding
parent gene. Pseudogenes are common in mammals, but virtually absent in Drosphila.28
Nineteen percent of the coding sequences identified in human chromosome 22 were
designated as pseudogenes, because they had significant similarity to known genes
or proteins but had disrupted protein coding reading frames. 82% appeared to be
processed pseudogenes.3 Many pseudogenes have additional mutations in
them, presumably because there is no functional constraint on their mutation. For
example, the human beta-tubulin gene family consists of 15–20 members, of
which five have these pseudogene hallmarks.29 Some pseudogenes affect
gene activity by binding transcriptional factors that activate the normal gene.
Whether this is intentional design or something the organism has simply adjusted
to is difficult to say. Many pseudogenes do seem to fit the profile of true junk
DNAs.

Figure 3. Comparison of integrated mobile DNA sequence structures.

Repetitive DNA sequences, including mobile DNA sequences

Repetitive DNA sequences form a substantial fraction of the genomes of many eukaryotes
(Table 1, Table 2).30,31 This class includes satellite DNA (very highly
repetitive, tandemly repeated sequences), minisatellite and microsatellite sequences
(moderately repetitive, tandemly repeated sequences), the new megasatellites (moderately
repetitive, tandem repeats of larger size) and transposable or mobile elements (moderately
repetitive, dispersed sequences that can move from site to site; see Table 2).

When first discovered, they did not seem to confer any benefit to the host organism,
as their ability to move about the genome and/or cause recombination between different
homologous copies has often resulted in deleterious mutation and disease. We now
know that at least some of these sequences carry out important functions.

Satellite sequences

The functionality of a sequence of 2 or 3 bp repeated a thousand or so times is
not immediately apparent. In addition, the lengths and compositions of these repetitions
often vary wildly between species, between organisms of the same species, or even
between cells of the same organism. But greater understanding has come as scientists
realize how DNA acts not only as the information source for the cell, but also as
the library in which it is housed.32 It is beginning to be seen that
the dispensability of sequences is not an indicator of their non-functionality,
and that in many cases, repetitive sequences tend to fill functions collectively
rather than individually.

Satellite sequences vary in their repeat size and in their array size (Table 2).
Microsatellites are the smallest, at a repeat size of as little as 2 bp, and the
newly discovered megasatellite sequences, which actually can contain ORFs, are 4–10
kb long.33 The actual sequence repeated differs from species to species,
and repeats can differ slightly from one another. The number in an array can vary
between individuals, which is why forensic DNA fingerprinting techniques use mini-
and microsatellite differences to identify individuals.

Table 2. Types of eukaryotic repetitive DNA sequences.

Functions of satellite sequences

The first recognised function of these types of sequences was in organising the
centromeres, the constricted sites on each chromosome where the chromosomes attach
to cellular tethers and are pulled apart during meiosis and mitosis. These sequences
help condense the DNA region they are in into heterochromatin*.

One hypothesis of the collective functionality of repeat sequences is that long
stretches of noncoding sequences act as tethers, permitting placement of groups
of genes into different zones in the cell nucleus.19 Transcriptionally
inactive heterochromatin and the heterochromatin-like telomeric sequences (sequences
at the end of chromosomes), may associate their respective chromatin segments much
of the time with the nuclear periphery. Very long runs of gene-poor, AT-rich isochores*, would be the tethers that permit
the gene-rich, GC-rich isochores to distribute themselves into the appropriate nuclear
zones for transcription and RNA processing.

The importance of the sequences of satellite DNA is reflected when these sequences
are mutated. A mutation in a minisatellite just after the end of the Harvey ras
gene (which encodes a growth regulatory protein) may contribute to as many as 10%
of all cases of breast, colo-rectal and bladder cancer, and acute leukemia. The
mutant minisatellites bind a transcriptional regulatory factor,34 which
causes an abnormal increase in transcription of the Harvey ras gene (Figure
4).

Figure 4. Mutations in minisatellite DNA can result in cancer. Mutated
satellite DNA near the Harvey ras gene (a major regulator of cell growth)
can bind a protein that increases ras activity.

These ‘class I mobile elements’ reproduce themselves through an RNA
intermediate which, in a reversal of the usual DNA to RNA transcription, is reverse
transcribed to DNA by the reverse transcriptase* enzyme encoded on intact elements. One of
the remarkable findings of the human genome project is that a high percentage (35.40%)
of human nuclear DNA consists of dispersed retroelements (Table 1).35
Short and long interspersed elements, SINEs and LINEs, make up the majority of this
class of DNA, with Alu and LINE-1 (L1), respectively, being most abundant
in humans.36 L1 elements encode their own reverse transcriptase, that
probably is also responsible for the spread of SINEs, which lack this enzyme. HIV-1,
the AIDS virus, human endogenous retroviruses* (HERVs), and solitary long terminal
repeats (LTRs*) apparently derived from HERVs,
are also part of this class of retroelements (Figure 3, Table 2).

Most eukaryotic retrotransposons*
move only sporadically in the genome. An exception is the hybrid dysgenesis seen
in Drosophila, where if flies containing a retrotransposon are mated to flies not
containing the particular retrotransposon, the element transposes with a high frequency,
resulting in death or mutation of many of the progeny. Host factors, many not well
characterized as yet, seem to keep the transposition rate in check (see below).

Functions of retroelements

Do these abundant elements have functions, or have hapless eukaryotic genomes been
parasitized by selfish DNA? There are more and more examples of these elements performing
important functions. One example is the Alu family. This 300-bp sequence
(named for the enzyme used to identify it) occurs almost a million times in the
human genome, up to 3.5% of the total DNA (Table 2). It is estimated, and has been
seen in many cloned genes, that there are 4 or 5 Alu elements in every
gene. Despite their number, they have been generally considered parasitic DNA, with
occasional deleterious effects on the genome when they exercise their ability to
retrotranspose to sites in and near genes, or recombine with each other abnormally.
Such disruptions have caused neurofibromatosis, or elephant man’s disease.16
Mutations in the Alu sequence also have been associated with cancer. Alu
sequences have been found to affect the functions of at least 8 different genes
(Table 2).37,38 Though Alu sequences do have internal promoters
for RNA polymerase III (an enzyme which transcribes genes encoding RNAs needed for
translation of mRNA into protein), normally very little RNA is produced from all
these Alu sequences. However, under certain stressful conditions such as
a viral infection, these transcripts increase dramatically and affect protein synthesis
levels to help the cell deal with the stress.39 Thus, though individual
Alu elements have a very weak effect, hundreds of thousands of them together
can affect protein synthesis.

Epigenetic control mechanisms, or modifications of gene activity that are due to
modifications of the DNA itself and not its sequence (see below), are associated
with repeats. A repeat-induced process involving L1 retroelements has been hypothesised
for X-chromosome inactivation, which is necessary to maintain proper gene dosage
in females, who have two X chromosomes (Table 2).40

Endogenous retroviruses (that is, those that are obtained from inheritance rather
than infection) can also affect gene expression. The LTRs of two such viruses provides
the sequence signal for the polyadenylation*
of the mRNA of two newly discovered human genes.41 An L1 repeat was found
to provide the polyadenylation signal for the mouse thymidylate synthase gene. Retrotransposons
were also seen to help in repairing chromosomal breaks in yeast. Retroelements modulate
expression of many more genes.42

DNA transposons, or ‘class II transposable elements’, move from place
to place by replicative transposition (that increases the copy number) or by a simple
cut-and-paste mechanism. Though in general not as common or in as high a copy number
as retroelements, they are still found in most organisms. Examples are the Drosophila
P elements, bacterial transposons such as Tn10 and Tn7, the Mu phage, and the ubiquitous
mariner/Tc1 superfamily of transposons. The mariner/Tc1 family is the most widespread,
being found in most insects, flatworms, nematodes, arthropods, ciliated protozoa,
fungi and many vertebrates, including zebra fish, trout and humans.43
Copy number varies from two copies in Drosophila sechellia, to 17,000 in
the horn fly Haematobia irritans, accounting for 1% of the genome. The
vast majority of them appear to have been inactivated by multiple mutations. The
close homology between mariner/Tc1 elements found in species thought to have diverged
200 million years ago has fuelled the hypothesis that these elements can transfer
horizontally (that is, not by normal inheritance) between different species, or
even different phyla (see below). Again, the evolutionist gets to pick and choose
from his smorgasbord of explanations when the data do not fit the evolutionary tree.

Miniature inverted-repeat transposable elements (MITEs)

A recently discovered third class of mobile elements is the miniature inverted-repeat
transposable elements (MITEs).44–46 They are very small (125–500
bp), and have short terminal inverted repeats. They were first found in plants,
but have also been found in nematodes, humans, mosquitoes and zebrafish.47–50
They are found in the thousands and tens of thousands per genome, and have been
given colourful names (e.g. Tourist, Stowaway, Alien and Bigfoot) to reflect their
apparent ability to move about in the genome. Their mechanism of transposition is
still unknown, but they appear to be DNA elements that cannot move about on their
own (non-autonomous). Though none seem to be presently active, they are believed
to have been mobile in the recent past because of the high levels of sequence similarity
between elements in a particular family, and the differences in insertion sites
seen in closely related species.51 MITEs are particularly interesting
in terms of generating genetic variation in that they are preferentially associated
with genes (see below).46,52

Effects of mobile and repetitive elements on gene expression

Mobile elements and repetitive elements can alter the structure and regulate expression
of the genome in several different ways. As described earlier, transposition can
disrupt genes by direct insertional mutagenesis and can adversely affect transcription.
Many retrotransposons have strong constitutive (always on) promoters that can cause
inappropriate expression of downstream genes. If the promoter is in the opposite
direction of the gene, RNA complementary to the mRNA of the gene can be made that
can act as antisense RNA*
that binds up the mRNA, affecting translation.

Figure 5. Recombination between direct repeats causes the loss of the DNA
between them.

Recombination between similar DNA strands is a necessary process for repair of DNA
breaks and allele* shuffling between
homologous chromosomes. But the presence of mobile and repetitive elements in inappropriate
positions can result in recombination products that are deleterious, such as translocations*, inversions*, and other chromosomal rearrangements (Figure 5).
For example, it was shown that a widespread chromosomal inversion commonly seen
in Drosophila buzzatii is caused by the recombination between two copies
of a transposable element in opposite orientations.53 There can even
be an exchange of DNA between non-homologous chromosomes: such as was seen in maize,
in this case mediated by the recombination of one complete and one partial copy
of the Ac (Activator) transposable element.54

Target site selection in mobile DNA

Many of the retrotransposons and DNA transposons seem to have very little site-specificity
in where they integrate.55 Integration sites for most mammalian and Drosophila
retroelements appear to be distributed more or less randomly in the genome. Vertebrate
retroviruses do have a general preference for insertion into regions with an open
chromatin configuration.56

However, there are some specific ones that do show target selectivity.51
R2 is a non-LTR retrotransposon that inserts preferentially in the 28S ribosomal
RNA genes of various insect species. Group II introns present in some yeast mitochondrial
genes (genes carried in the energy-producing organelles in the cell), are mobile
elements very similar to poly (A)-type retrotransposons. After copying themselves,
they can reinsert precisely back into their spots between two exons. Their ability
to move argues for their spread into various genes at some point in time. The yeast
retrotransposons Tyl and Ty3, integrate preferentially upstream of genes transcribed
by RNA polymerase III, which transcribes genes needed for protein synthesis.

Very recently, evidence has been found that certain P elements* containing regulatory sequences from developmental
genes, showed a high frequency of reinserting at the parent gene (homing) and preferential
insertion at another site containing regulatory genes.57

The first example known of a host using the movement of a retrotransposon to its
advantage, was found in the telomere maintenance of Drosophila. The telomeres,
or chromosomal ends of Drosophila, are maintained differently than any
other known organism. Two retroposons, HeTA and TART, are present in multiple copies
on the telomeres, and will retropose specifically to the end of the telomere and
heal a frayed chromosome.58

Observed regulation of mobile DNA

Epigenetic mechanisms, or reversible but heritable changes in chromatin structure,
are seen to play a role in regulating genes. Methylation of cytosine residues, modification
of the DNA-binding histones, and production of antisense RNAs, are some of the mechanisms
by which gene expression can be modified without permanent genetic change to the
gene regulated.59 Methylation of the cytosine residues of DNA is used
by the cell to turn off genes not currently needed. Cytosine methylation inactivates
the promoters of most viruses and transposons (including retroviruses and Alu
elements). In fact, transposons are so abundant, rich in CpG dinucleotides and heavily
methylated, that we now know that the large majority of 5'-methylcytosine in the
genome actually lies within these elements.60 This prevents the movement
of the elements under normal circumstances. Thus transposable elements that integrate
into promoters of genes can alter gene expression patterns by attracting methylation
or chromatin modifications to regulate the modified promoter.53

Drosophila, in general, are very vulnerable to mutation by mobile element
activity. From 50–85% of all spontaneous mutations seen in the fruit fly are
due to transposon insertions.53 But Drosophila does have one
type of host control in the recently identified gene named flamenco. Flamenco
normally acts to keep the gypsy retrotransposon in check. When flamenco
is mutated, gypsy transposes at a high frequency in germ line (reproductive) cells.50

Criteria for identifying junk DNA

There are several possible scenarios for the presence and function of the putative
junk DNA sequences described above:

They all perform God-designed functions in present day organisms in their present
form and location, though current research has not revealed what those are as yet.
This is unlikely, as it seems clear that in some individuals and species, the placement
or particular sequence of one of a family of non-coding DNAs can lead to deleterious
effects such as cancer and genetic disease. This would contradict the Bible’s
description of God’s original perfect creation.

All non-coding sequences could have been created with functions, but some have lost
their functions due to God’s purposeful limitations, and/or accumulation of
mutations post-Fall. This would fit in with our observation of the rest of creation,
where, though the perfection of God’s design can be seen, it has become obscured
by consequences of the Fall, allowing death and suffering to enter the world.

There is the possibility that some of the elements, such as the mobile elements
in particular, have never had designed functions. Rather, they are pieces of degenerate
DNA affected by the Fall that randomly move about and mutate genomes, causing only
deleterious effects.

The ability of DNA sequences to rearrange and/or to move about in the genome or
even between genomes, was originally a heretical idea for both evolutionist and
creationist, but now is one that is strongly supported as being an integral part
of gene regulation. Many systems utilizing similar recombination and rearrangement
mechanisms are necessary for important cellular functions, such as the process of
DNA repair, rearrangement of DNA segments to form the genes for the thousands of
different antibodies, the yeast mating type switching system, the flagellar switching
system of Salmonella, and the antigen switching system of the malaria parasite.
Therefore, the second scenario seems the most likely.

A working list of criteria needs to be developed to attempt to identify DNA sequences
that may actually fit the category of junk DNA. The presence of some junk DNA would
be expected due to the fallen state of genomes. True junk DNA may have one or more
of the following characteristics:

The DNA element is present within another gene, insertionally inactivating it.

The DNA element is not found at that location in other members within the same species.

The effects of the presence of the element, if known, are deleterious, e.g. lead
to cancer, genetic disease, etc.

The element can be deleted without any observed ill effects on the organism or many
generations of its descendants.

The sequence of the element closely matches that of a mobile element, or contains
a mobile element sequence.

For example, pseudogenes have many of these junk DNA characteristics, though their
transformation into junk DNA may in some cases have been intentionally arranged
by God for the purpose of rapid diversification of created kinds.

The AGEing theory and diversification

There are, as described above, instances of functions for transposable DNAs, but
until recently there has not been a particular purpose ascribed to repetitive and
mobile elements as a group. A new hypothesis formulated by genomicist and creationist
Wood addresses the past and present functions of mobile and repetitive DNA.61

Since these elements are capable of rapid change of the genome, and can even be
transmitted horizontally between species, he proposes that God designed them to
move about or recombine in the genomes of organisms to allow the rapid intrabaraminic
diversification seen in the 500 years or so after the Flood. He sees their role
as being designed to act for a limited period of time, after which they would be
inactivated by mutation or repression by other regulatory elements. He proposes
that such elements should be renamed Altruistic Genetic Elements (AGEs) to emphasize
that their purpose is different than that proposed for ‘selfish’ DNA.

The AGEs are hypothesised to work by activating dormant genes or inactivating active
genes, or by horizontally transferring genetic information between species or possibly
baramins with AGEs in the form of mobile elements. The phenotypic changes would
be primarily cosmetic, such as variations in size or coloration, or would involve
activation of a complex of genes needed to utilize a new environmental niche, like
the Arctic fox’s adaptation to cold. There is a need for creationists to explain
how a holobaramin such as the cat family,62 could diversify into the
many species of cats that were present even in Job’s time in just a few thousand
years or possibly a few hundred years. Currently observed genetic mechanisms and
natural selection are far too slow to explain this rapid speciation. A limited time
period of AGE activity could explain how this rapid diversification could occur.

If, for example, the proposed AGEs were at work in the diversification of the equines,
we have the testable predication that differences in size, morphology and coloration
could be traced back to the genetic level by mobile or repetitive DNA elements located
near genes controlling coloration. Pseudogenes and relic retroviral sequences could
then be the result of the action of an AGE gone wrong after its designed activity
began to fail. The AGEing theory could also solve the ‘founding pair’
problem—that is, when a rare macromutation occurs in an individual such that
it cannot successfully hybridise with its parental species, this mutation is lost
unless it can mate with another animal with the same mutation.

For this proposed AGEing process to work, at least three things must be observed
in putative AGEs:

They must show site specificity in where they insert, or evidence that they had
such specificity in the past.

Transmission of AGEs between organisms horizontally and into germline DNA is required.

We should see AGEs associated with genes affecting size, morphology, coloration,
and specialised environmental adaptation rather than housekeeping genes.

As for the first requirement, though many mobile elements are not specific in their
target sites, there are examples of those that are, as discussed above. Since AGE
movement is supposed to have occurred largely in the past, we might expect to see
only a few with the intact capability.

As for the second requirement, horizontal transmission*, the evidence for that occurring has become
very strong,63 and in the case of the P and gypsy elements in Drosophila,
such transmission has actually been observed occurring between species. Originally,
no wild-caught D. melanogaster contained the P element and laboratory
stocks collected 60 years ago reflected this. Then gradually, more and more wild-caught
flies contained the element originally found in D. willistoni, until now
all wild flies even in remote locations contain this element.64 Recently,
it was also shown that the copia retrotransposon from D. melanogaster
was transferred to D. willistoni (probably via a parasitic mite).65,66
There was also a report that gypsy-free fruit flies permissive for transposition
of the gypsy retroposon could incorporate gypsy into their germline DNA when larvae
were fed on extract of infected pupae.67 There is no obvious evidence
pointing to a functional change mediated by these horizontal transfers, but the
principle is there.

As for the third requirement, are there any examples known now of mobile or repetitive
elements that can cause these types of phenotypic changes? In bacteria, there are
many examples of transfers of antibiotic resistance mediated by transposons,68
and the horizontal transfer of genes, though in general prokaryotes have comparatively
little ‘junk’ DNA. Some evolutionary researchers now propose that mobile
elements may be involved in speciation. Mobility of a retroelement was activated
in a cross between two wallaby species, though the hybridisation resulted in only
sterile males.69 In maize, the original studies of Nobel Prize winner
Barbara McClintock demonstrated that the activity of the transposons in different
corn kernel cells could be followed by their effects on corn kernel coloration.
In plants, there is additional strong evidence that movement of mobile elements
in the past has altered gene expression. Although retrotransposon sequences, for
example, are seldom found near genes in animals, recent analyses of plant mobile
element insertion sites have revealed the presence of degenerate retrotransposon
insertions adjacent to many normal plant genes that act as regulatory elements.70
In addition to retrotransposons, MITEs are also found adjacent to many plant genes,
where they also often provide regulatory sequences necessary for transcription.71
Plants, as well as animals, would have had to adjust to the drastically-altered
post-Flood world. Other, more dramatic examples may exist, and further research
will hopefully reveal them.

AGEing activity during the Ark sojourn

Putting thousands of animals aboard the Ark could have had a dual purpose. Not only
did it preserve their lives, but also it would probably allow transfer of genetic
material and/or activation of latent genes simultaneously in all land animals. Under
the relatively crowded Ark conditions, transfer of genetic material from one species
to another through broad host range viruses, parasitic mites or fleas would be facilitated.
This might have produced a distribution of AGEs in species in such a way as to defy
evolutionary phylogeny, as is seen for the Tc1/mariner family and in the gypsy family
of retrotransposons.72

Why debunk ‘junk’ DNA?

What is the relevance to creation science, and to Christians in general, of a better
understanding of the function of these DNA elements? Because of the publicity surrounding
the Human Genome Project, there is increasing general interest in how our genomes
work, and what exactly they look like. There is more and more emphasis being placed
on discovering our evolutionary history through DNA, not fossils.

The fact that functions are being found for junk DNAs fits in well with creation
science, but was not predicted by evolutionary theory, though of course the theory
is being adjusted again to accommodate the data. The intricate flexibility and specificity
of these ‘junk’ DNA sequences are a strong testimony to a Creator who
plans and provides for the future of his creation.

Glossary

Allele

one of several alternate forms of a gene occupying a given locus on a chromosome.
Return to text.

Antisense RNA

RNA made by copying the other DNA strand in a coding segment in the opposite direction;
this RNA will bind to the mRNA made from the coding or sense strand.
Return to text.

Baramin

the creationist term for an original created kind as described in Genesis; not synonymous
with species. Organisms within the same baramin may be of different species but
can cross-hybridise, like the horse and the donkey. Return to text.

Complementary

two strands of DNA or RNA are said to be complementary when they can form base pairs
(A-T, G-C) with each other, e.g. AATTCC and TTAAGG. Return
to text.

Chromatin

the complex of DNA and protein in the nucleus of the interphase cell.
Return to text.

Euchromatin

the less condensed chromatin in the nucleus that is more transcriptionally active
than the heterochromatin. Return to text.

half the set of the chromosome pairs; contains one copy of each chromosome pair
and one of the sex chromosomes; characteristic of gametes (sperm and egg cells).
Return to text.

Heterochromatin

regions of the genome that are in a highly condensed state and are not usually transcribed.
Constitutive hetereochromatin is always in this condensed, inactive state, contains
no genes, and is usually found at the centromeres and teleomeres. Facultative heterochromatin
is condensed only in certain cell types, or at certain developmental stages when
the genes contained in it need to be turned off. Return
to text.

Histones

a family of basic proteins found tightly associated with DNA in all eukaryotic nuclei;
their binding forms a bead structure called a nucleosome. Return
to text.

Horizontal transmission

when mobile elements or viruses are transferred between individuals by infection
rather than by inheritance (vertical transmission).
Return to text.

Human endogenous retroviruses (HERVs)

retroviruses that have become part of the human genome in the past by insertion
into the germline cells. Return to text
.

Hybridisation

the pairing of single-stranded complementary RNA and/or DNA strands to give an RNA-DNA
or DNA-DNA hybrid. Return to text.

Inversion

occurs when recombination between DNA segments causes the DNA between them to be
flipped into the opposite orientation at the same chromosomal locus.
Return to text.

Isochore

an approximately 300 kb segment of DNA whose bp composition is uniform above a 3
kb level, for example 67% A-T bp. This is believed to enable a certain level of
co-regulation of all the DNA in the isochore. Return to text
.

LTR

long terminal repeat; the longer, more complex repeated sequences at the ends of
some mobile elements, which are required for them to transpose. Return
to text.

ORF

open reading frame; a stretch of DNA or RNA that contains of series of triplet codons
coding for amino acids, without any protein termination codons, that is potentially
translatable into protein. Return to text.

P elements

DNA transposons found in fruit fly species that often have a high level of mobility.
Return to text.

Promoter

a region of DNA involved in binding of RNA polymerase to initiate transcription.
Return to text.

Poly-(A) tail

a sequence of adenine residues added to the 3’ end of a mRNA after transcription
in the process called polyadenylation; believed to help stabilize mRNAs from being
degraded. Return to text.

Pseudogene

a gene that has been inactivated in the past by an insertion or deletion of DNA.
Return to text.

Prokaryote

an organism that lacks an organized nucleus, and has its DNA mostly in a single
molecule; a bacterium. Return to text.

Processed pseudogene

a gene that has been apparently reverse-transcribed from its mRNA back into DNA
and reinserted into a chromosome. It thus lacks its introns, has a poly-A tail,
and often is bounded by the characteristic direct repeats associated with transposition.
Return to text.

mobile elements that encode reverse transcriptase. Transpose through an RNA intermediate.
Classed into LTR-containing and poly (A)- containing:LTR-containing—similar to proviral form of vertebrate retroviruses
and usually have 2 ORFs, gag and pol (protease, integrase, reverse
transcriptase, RNase H), e.g. Gypsy and tom.Poly (A)—containing retroelements or retroposons lack LTRs
and have a 3’ A-rich region. Have 2 ORFs, gag and pol. Some elements such
as L1 and the I Factor of Drosophila, contain a reverse transcriptase.
L1 is found in yeast and humans. Return to text
.

Retrovirus

a virus using RNA as its information storage system rather than DNA, integrates
into host DNA as part of its lifecycle in a way very similar to retrotransposons,
but also has additional genes that code for its packaging into virus particles for
infection of other hosts. Return to text.

Reverse transcriptase

an enzyme found in retroelements that will make a complementary DNA strand from
an RNA template. Return to text.

Splicing

two exons, or coding regions on a messenger RNA, are joined together when the intron
(non-coding segment) between them is removed. Return to text
.

Translation

the synthesis of protein on the messenger RNA template. Return
to text.

Translocation

of a chromosome describes a rearrangement in which part of a chromosome is detached
by breakage and then becomes attached to some other chromosome.
Return to text.

the enzyme that cuts the target DNA and splices in the transposing sequence; called
the integrase in retroelements.

Transposon

any DNA sequence that can move about the genome, either by replicating itself, or
by a cut-and-paste mechanism. In its simplest form, it is a transposase gene (see
above) surrounded by a sequence on either side repeated directly or in inverse form,
e.g. ATTGCGC and CGCGTTA are inverted repeats. Return to text
.

Triplet codon

three nucleotides in an RNA or DNA that signal the insertion of a particular amino
acid or termination signal; e.g. AUG would be the ‘code word’ for methionine.
Return to text.

UTR

untranslated region; the parts of a messenger RNA before the first exon (‘5
prime’ UTR) and after the last exon (‘3 prime’ UTR) that are not
translated into protein (non-coding). Return to text.

Acknowledgements

The author wishes to thank Dr. Todd C. Wood for providing unpublished information
on his AGEing theory and his rice genome research. Thanks also to the editor for
helpful discussions, information and patience with revisions.

Each amino acid attached to a transfer RNA can be added onto a protein when the
transfer RNA anticodon recognizes the complementary three nucleotides (a ‘word’)
in the mRNA. Since there are only 20 amino acids and there are 64 possible trinucleotide
combinations or ‘words’, several triplet codons can code for the insertion
of one amino acid. This redundancy allows some variation in G-C content in a gene
without changing the composition of the protein produced.

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